Reticular formation: This is a large area in the midbrain that is involved in various important functions of the midbrain. In particular, it contains lower motor neurons, is involved in the pain desensitization pathway, is involved in the arousal and consciousness systems, and contains the locus coeruleus, which is involved in intensive alertness modulation and in autonomic reflexes.

Superior to the obex is the floor of the fourth ventricle. In the floor of the fourth ventricle, various nuclei can be visualized by the small bumps that they make in the overlying tissue. In the midline and directly superior to the obex is the vagal trigone and superior to that it the hypoglossal trigone. Underlying each of these are motor nuclei for the respective cranial nerves. Superior to these trigones are fibers running laterally in both directions. These fibers are known collectively as the striae medullares. Continuing in a rostral direction, the large bumps are called the facial colliculi. Each facial colliculus, contrary to their names, do not contain the facial nerve nuclei. Instead, they have facial nerve axons traversing superficial to underlying abducens (CN VI) nuclei. Lateral to all these bumps previously discussed is an indented line, or sulcus that runs rostrally, and is known as the sulcus limitans. This separates the medial motor neurons from the lateral sensory neurons. Lateral to the sulcus limitans is the area of the vestibular system, which is involved in special sensation. Moving rostrally, the inferior, middle, and superior cerebellar peduncles are found connecting the midbrain to the cerebellum. Directly rostral to the superior cerebellar peduncle, there is the superior medullary velum and then the two trochlear nerves. This marks the end of the pons as the inferior colliculus is directly rostral and marks the caudal midbrain. Middle cerebellar peduncle is located inferior and lateral to the superior cerebellar peduncle, connecting pons to the cerebellum. Likewise, inferior cerebellar peduncle is found connecting the medulla oblongata to the cerebellum.

The adult human brainstem emerges from two of the three primary vesicles formed of the neural tube. The mesencephalon is the second of the three primary vesicles, and does not further differentiate into a secondary vesicle. This will become the midbrain. The third primary vesicle, the rhombencephalon (hindbrain) will further differentiate into two secondary vesicles, the metencephalon and the myelencephalon. The metencephalon will become the cerebellum and the pons. The more caudal myelencephalon will become the medulla.

The brainstem plays a role in conduction. That is, all information relayed from the body to the cerebrum and cerebellum and vice versa must traverse the brainstem. The ascending pathways coming from the body to the brain are the sensory pathways and include the spinothalamic tract for pain and temperature sensation and the dorsal column-medial lemniscus pathway (DCML) including the gracile fasciculus and the cuneate fasciculus for touch, proprioception, and pressure sensation. The facial sensations have similar pathways and will travel in the spinothalamic tract and the DCML. Descending tracts are the axons of upper motor neurons destined to synapse on lower motor neurons in the ventral horn and posterior horn. In addition, there are upper motor neurons that originate in the brainstem's vestibular, red, tectal, and reticular nuclei, which also descend and synapse in the spinal cord.

The cranial nerves III-XII emerge from the brainstem.[4] These cranial nerves supply the face, head, and viscera. (The first two pairs of cranial nerves arise from the cerebrum).

The brainstem has integrative functions being involved in cardiovascular system control, respiratory control, pain sensitivity control, alertness, awareness, and consciousness. Thus, brainstem damage is a very serious and often life-threatening problem.

Ten of the twelve pairs of cranial nerves either target or are sourced from the brainstem.[5] The nuclei of the oculomotor nerve (III) and trochlear nerve (IV) are located in the midbrain. The nuclei of the trigeminal nerve (V), abducens nerve (VI), facial nerve (VII) and vestibulocochlear nerve (VIII) are located in the pons. The nuclei of the glossopharyngeal nerve (IX), vagus nerve (X), accessory nerve (XI) and hypoglossal nerve (XII) are located in the medulla. The fibers of these cranial nerves exit the brainstem from these nuclei.[6]

Diseases of the brainstem can result in abnormalities in the function of cranial nerves that may lead to visual disturbances, pupil abnormalities, changes in sensation, muscle weakness, hearing problems, vertigo, swallowing and speech difficulty, voice change, and co-ordination problems. Localizing neurological lesions in the brainstem may be very precise, although it relies on a clear understanding on the functions of brainstem anatomical structures and how to test them.

Duret haemorrhages are areas of bleeding in the midbrain and upper pons due to a downward traumatic displacement of the brainstem.[7]

Cysts known as syrinxes can affect the brainstem, in a condition, called syringobulbia. These fluid-filled cavities can be congenital, acquired or the result of a tumor.

Criteria for claiming brainstem death in the UK have developed in order to make the decision of when to stop ventilation of somebody who could not otherwise sustain life. These determining factors are that the patient is irreversibly unconscious and incapable of breathing unaided. All other possible causes must be ruled out that might otherwise indicate a temporary condition. The state of irreversible brain damage has to be unequivocal. There are brainstem reflexes that are checked for by two senior doctors so that imaging technology is unnecessary. The absence of the cough and gag reflexes, of the corneal reflex and the vestibulo–ocular reflex need to be established; the pupils of the eyes must be fixed and dilated; there must be an absence of motor response to stimulation and an absence of breathing marked by concentrations of carbon dioxide in the arterial blood. All of these tests must be repeated after a certain time before death can be declared.[8]